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    Sdk1 sidekick cell adhesion molecule 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304297, updated on 14-Nov-2024

    Summary

    Official Symbol
    Sdk1provided by RGD
    Official Full Name
    sidekick cell adhesion molecule 1provided by RGD
    Primary source
    RGD:1560686
    See related
    EnsemblRapid:ENSRNOG00000001103 AllianceGenome:RGD:1560686
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1560686
    Summary
    Predicted to act upstream of or within behavioral response to cocaine and regulation of dendritic spine development. Predicted to be located in membrane. Orthologous to human SDK1 (sidekick cell adhesion molecule 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 108.4), Kidney (RPKM 27.3) and 7 other tissues See more
    Orthologs
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    Genomic context

    See Sdk1 in Genome Data Viewer
    Location:
    12q11
    Exon count:
    47
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (17491430..18477914, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (12378074..13363934, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (14445798..15443442, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095892 Neighboring gene forkhead box K1 Neighboring gene ubiquitin-conjugating enzyme E2C, pseudogene 2 Neighboring gene uncharacterized LOC134481157 Neighboring gene U6 spliceosomal RNA Neighboring gene glyceraldehyde-3-phosphate dehydrogenase-like Neighboring gene uncharacterized LOC120095893 Neighboring gene nucleolar pre-rRNA processing protein NIP7, pseudogene 9

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    acts_upstream_of_or_within behavioral response to cocaine ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within regulation of dendritic spine development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      17491430..18477914 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271861.1XP_063127931.1  protein sidekick-1 isoform X2

      Related
      ENSRNOP00000109822.1, ENSRNOT00000136830.1
    2. XM_039089863.2XP_038945791.1  protein sidekick-1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A427
      Related
      ENSRNOP00000086581.1, ENSRNOT00000089775.3
      Conserved Domains (7) summary
      PHA03307
      Location:38162
      PHA03307; transcriptional regulator ICP4; Provisional
      cd00063
      Location:17991892
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:765850
      fn3; Fibronectin type III domain
      pfam07679
      Location:575665
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:388460
      Ig_3; Immunoglobulin domain
      cd00096
      Location:583586
      Ig; Ig strand A' [structural motif]
      cl11960
      Location:481570
      Ig; Immunoglobulin domain
    3. XM_039089864.2XP_038945792.1  protein sidekick-1 isoform X3

      Related
      ENSRNOP00000112178.1, ENSRNOT00000169334.1
      Conserved Domains (6) summary
      cd00063
      Location:14141507
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:380465
      fn3; Fibronectin type III domain
      pfam07679
      Location:190280
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:375
      Ig_3; Immunoglobulin domain
      cd00096
      Location:198201
      Ig; Ig strand A' [structural motif]
      cl11960
      Location:96185
      Ig; Immunoglobulin domain
    4. XM_063271862.1XP_063127932.1  protein sidekick-1 isoform X3